Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)

RGD DISEASE ONTOLOGY - ANNOTATIONS

RGD uses the Human Disease Ontology (DO, https://disease-ontology.org/) for disease curation across species. RGD automatically downloads each new release of the ontology on a monthly basis. Some additional terms which are required for RGD's curation purposes but are not currently covered in the official version of DO have been added. As corresponding terms are added to DO, these custom terms are retired and the DO terms substituted in existing annotations and subsequently used for curation.
Term:urolithiasis
go back to main search page
Accession:DOID:0080653 term browser browse the term
Definition:A urinary system disease that is characterized by the formation of stony concretions in the bladder or urinary tract. (DO)
Synonyms:exact_synonym: urinary lithiasis
 primary_id: MESH:D052878
 alt_id: DOID:9001149;   OMIA:001033
 xref: NCI:C114688


show annotations for term's descendants           Sort by:
urolithiasis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G APRT adenine phosphoribosyltransferase EXP CTD Direct Evidence: marker/mechanism CTD PMID:7766 PMID:3876264 NCBI chr16:88,809,339...88,811,928
Ensembl chr16:88,809,339...88,811,937 		JBrowse link
G GGCX gamma-glutamyl carboxylase ISO
EXP		 protein:increased activity:kidney:
CTD Direct Evidence: marker/mechanism		 CTD
RGD		 PMID:9471053 PMID:9471053 RGD:11040514 NCBI chr 2:85,544,720...85,561,493
Ensembl chr 2:85,544,720...85,561,532 		JBrowse link
G PLAU plasminogen activator, urokinase IAGP DNA:snp:3' utr:g.4065C>T (human) RGD PMID:18240004 RGD:7241142 NCBI chr10:73,909,164...73,917,494
Ensembl chr10:73,909,177...73,917,496 		JBrowse link
G SLC26A1 solute carrier family 26 member 1 EXP CTD Direct Evidence: marker/mechanism CTD PMID:19002488 PMID:20160351 NCBI chr 4:978,991...993,404
Ensembl chr 4:979,073...993,440 		JBrowse link
G SLC2A9 solute carrier family 2 member 9 ISO Urolithiasis OMIA PMID:15501150 PMID:38133239 NCBI chr 4:9,771,025...10,040,270
Ensembl chr 4:9,771,153...10,054,936 		JBrowse link
adenine phosphoribosyltransferase deficiency term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G APRT adenine phosphoribosyltransferase IAGP
ISS
EXP		 ClinVar Annotator: match by term: Adenine phosphoribosyltransferase deficiency
OMIM:614723
CTD Direct Evidence: marker/mechanism		 ClinVar
MouseDO
CTD
OMIM		 PMID:1353080 PMID:1673292 PMID:1781410 PMID:1985452 PMID:2135300 More... NCBI chr16:88,809,339...88,811,928
Ensembl chr16:88,809,339...88,811,937 		JBrowse link
G CDT1 chromatin licensing and DNA replication factor 1 IAGP ClinVar Annotator: match by term: Adenine phosphoribosyltransferase deficiency ClinVar PMID:25741868 PMID:28492532 NCBI chr16:88,803,789...88,809,258
Ensembl chr16:88,803,789...88,809,258 		JBrowse link
G GALNS galactosamine (N-acetyl)-6-sulfatase IAGP ClinVar Annotator: match by term: Adenine phosphoribosyltransferase deficiency ClinVar PMID:25741868 PMID:28492532 NCBI chr16:88,813,734...88,856,947
Ensembl chr16:88,813,734...88,856,970 		JBrowse link
G LOC130059760 ATAC-STARR-seq lymphoblastoid silent region 7879 IAGP ClinVar Annotator: match by term: Adenine phosphoribosyltransferase deficiency ClinVar PMID:7912608 PMID:20150536 PMID:21304254 PMID:22988602 PMID:25741868 More... NCBI chr16:88,811,681...88,812,080 JBrowse link
AZOOSPERMIA, OBSTRUCTIVE, WITH NEPHROLITHIASIS term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G CLDN2 claudin 2 IAGP ClinVar Annotator: match by term: Azoospermia, obstructive, with nephrolithiasis ClinVar
OMIM		 PMID:31320686 NCBI chr  X:106,900,164...106,930,861
Ensembl chr  X:106,900,164...106,930,861 		JBrowse link
bladder calculus term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G AHR aryl hydrocarbon receptor EXP CTD Direct Evidence: marker/mechanism CTD PMID:22232670 NCBI chr 7:17,298,652...17,346,147
Ensembl chr 7:16,916,359...17,346,152 		JBrowse link
calcium oxalate nephrolithiasis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G AMBP alpha-1-microglobulin/bikunin precursor IEP
ISO		 protein:increased expression:urine RGD PMID:16622176 PMID:15533056 RGD:6904147, RGD:6904219 NCBI chr 9:114,060,127...114,078,300
Ensembl chr 9:114,060,127...114,078,328 		JBrowse link
G BGLAP bone gamma-carboxyglutamate protein IEP protein:increased expression:serum: RGD PMID:21908029 RGD:7207408 NCBI chr 1:156,242,184...156,243,317
Ensembl chr 1:156,242,184...156,243,317 		JBrowse link
G CASR calcium sensing receptor susceptibility IAGP DNA:missense mutation:cds:p.R990G (rs1042636)(human)
associated with Hyperparathyroidism, Primary; DNA:snp:intron:IVS1 G>A rs1501899 (human)
DNA:snp:intron:IVS4+11988A>G rs17251221 (human)
DNA:missense mutations:cds:p.A986S, p.E1011Q (human)		 RGD PMID:17018660 PMID:21183554 PMID:21966463 PMID:20602573 RGD:13464331, RGD:7205447, RGD:7205446, RGD:7205445 NCBI chr 3:122,183,668...122,291,629
Ensembl chr 3:122,183,668...122,291,629 		JBrowse link
G CAT catalase ISO RGD PMID:21557843 RGD:7205663 NCBI chr11:34,438,934...34,472,060
Ensembl chr11:34,438,934...34,472,060 		JBrowse link
G F2 coagulation factor II, thrombin ISO mRNA:decreased expression:kidney RGD PMID:16981243 RGD:6893592 NCBI chr11:46,719,213...46,739,506
Ensembl chr11:46,719,196...46,739,506 		JBrowse link
G FN1 fibronectin 1 IAGP
ISO		 DNA:polymorphism: :
protein:increased expression:kidney		 RGD PMID:19616291 PMID:11025758 RGD:7206842, RGD:7206846 NCBI chr 2:215,360,865...215,436,068
Ensembl chr 2:215,360,440...215,436,073 		JBrowse link
G IDUA alpha-L-iduronidase IAGP ClinVar Annotator: match by term: Calcium oxalate nephrolithiasis ClinVar PMID:25741868 PMID:27210743 PMID:28492532 PMID:30586318 PMID:36719378 NCBI chr 4:986,997...1,008,351
Ensembl chr 4:986,997...1,004,564 		JBrowse link
G IL1RN interleukin 1 receptor antagonist IAGP DNA:repeats:intron:IVS2+914_1000dup IL1RN*1 (human) RGD PMID:17258699 RGD:6907128 NCBI chr 2:113,099,360...113,134,014
Ensembl chr 2:113,099,315...113,134,016 		JBrowse link
G PTH parathyroid hormone IEP protein:decreased expression:serum (human) RGD PMID:23470222 RGD:7242417 NCBI chr11:13,492,054...13,496,181
Ensembl chr11:13,492,054...13,496,181 		JBrowse link
G SLC26A1 solute carrier family 26 member 1 EXP
IAGP		 CTD Direct Evidence: marker/mechanism
ClinVar Annotator: match by term: Calcium oxalate nephrolithiasis		 CTD
ClinVar		 PMID:25741868 PMID:27210743 PMID:28492532 PMID:30586318 PMID:36719378 NCBI chr 4:978,991...993,404
Ensembl chr 4:979,073...993,440 		JBrowse link
Calcium Oxalate Nephrolithiasis 1 term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G IDUA alpha-L-iduronidase IAGP ClinVar Annotator: match by term: NEPHROLITHIASIS, CALCIUM OXALATE, 1 ClinVar PMID:25741868 PMID:28492532 NCBI chr 4:986,997...1,008,351
Ensembl chr 4:986,997...1,004,564 		JBrowse link
G SLC26A1 solute carrier family 26 member 1 IAGP ClinVar Annotator: match by term: NEPHROLITHIASIS, CALCIUM OXALATE, 1 OMIM
ClinVar		 PMID:25741868 PMID:28492532 NCBI chr 4:978,991...993,404
Ensembl chr 4:979,073...993,440 		JBrowse link
Calcium Oxalate Nephrolithiasis 2 with Nephrocalcinosis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G OXGR1 oxoglutarate receptor 1 IAGP ClinVar Annotator: match by term: Nephrolithiasis, calcium oxalate, 2, with or without nephrocalcinosis OMIM
ClinVar		 PMID:36571463 NCBI chr13:96,985,713...96,994,730
Ensembl chr13:96,985,713...96,994,730 		JBrowse link
cystinuria term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G CENPF centromere protein F IAGP ClinVar Annotator: match by term: Cystinuria ClinVar PMID:25741868 NCBI chr 1:214,603,195...214,664,571
Ensembl chr 1:214,603,185...214,664,574 		JBrowse link
G CEP89 centrosomal protein 89 IAGP ClinVar Annotator: match by term: Cystinuria ClinVar PMID:21681106 NCBI chr19:32,875,925...32,971,958
Ensembl chr19:32,875,925...32,971,991 		JBrowse link
G PREPL prolyl endopeptidase like IAGP ClinVar Annotator: match by term: Cystinuria
ClinVar Annotator: match by term: Cystinuria, non-type I
ClinVar Annotator: match by term: Cystinuria | ClinVar Annotator: match by term: Cystinuria, non-type I		 ClinVar PMID:7573036 PMID:8054986 PMID:8792820 PMID:9648062 PMID:9768685 More... NCBI chr 2:44,317,607...44,361,862
Ensembl chr 2:44,316,281...44,361,862 		JBrowse link
G SLC3A1 solute carrier family 3 member 1 susceptibility IAGP
ISS
EXP		 DNA:missense mutations
ClinVar Annotator: match by term: Cystinuria, non-type I
ClinVar Annotator: match by term: Cystinuria | ClinVar Annotator: match by term: Cystinuria, non-type I
ClinVar Annotator: match by term: Cystine urolithiasis | ClinVar Annotator: match by term: Cystinuria
OMIM:220100
CTD Direct Evidence: marker/mechanism		 ClinVar
MouseDO
CTD
OMIM
RGD		 PMID:7539209 PMID:7573036 PMID:8054986 PMID:8731106 PMID:8792820 More... RGD:1600015 NCBI chr 2:44,275,480...44,322,437
Ensembl chr 2:44,275,458...44,321,494 		JBrowse link
G SLC7A9 solute carrier family 7 member 9 IAGP
ISS
EXP		 DNA:missense mutations, nonsense mutations:cds:multiple (human)
ClinVar Annotator: match by term: Cystinuria
ClinVar Annotator: match by term: Cystine urolithiasis | ClinVar Annotator: match by term: Cystinuria | ClinVar Annotator: match by term: SLC7A9-related condition
ClinVar Annotator: match by term: Cystinuria | ClinVar Annotator: match by term: Cystinuria, non-type I
OMIM:220100
CTD Direct Evidence: marker/mechanism		 ClinVar
MouseDO
CTD
OMIM
RGD		 PMID:6031738 PMID:9536098 PMID:10471498 PMID:11013083 PMID:11157794 More... RGD:737767 NCBI chr19:32,830,511...32,869,767
Ensembl chr19:32,830,509...32,869,767 		JBrowse link
Dent disease term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G CLCN5 chloride voltage-gated channel 5 IAGP
ISS
EXP		 ClinVar Annotator: match by term: Dent disease
ClinVar Annotator: match by term: Dent's disease
OMIM:300009 | OMIM:300555
CTD Direct Evidence: marker/mechanism		 ClinVar
MouseDO
CTD		 PMID:10561751 PMID:11136179 PMID:15719255 PMID:15814539 PMID:15895257 More... NCBI chr  X:49,922,596...50,099,230
Ensembl chr  X:49,922,596...50,099,235 		JBrowse link
G LOC126863258 BRD4-independent group 4 enhancer GRCh37_chrX:49854497-49855696 IAGP ClinVar Annotator: match by term: Dent's disease
ClinVar Annotator: match by term: Dent disease		 ClinVar PMID:11136179 PMID:15719255 PMID:15895257 PMID:16822791 PMID:18038239 More... NCBI chr  X:50,089,840...50,091,039 JBrowse link
G OCRL OCRL inositol polyphosphate-5-phosphatase IAGP ClinVar Annotator: match by term: Dent disease ClinVar PMID:15108291 PMID:21031565 PMID:21971085 PMID:27398910 PMID:29300302 NCBI chr  X:129,540,259...129,592,556
Ensembl chr  X:129,539,849...129,592,561 		JBrowse link
Dent disease 1 term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G CLCN5 chloride voltage-gated channel 5 IAGP
EXP		 ClinVar Annotator: match by term: Nephrolithiasis 2
ClinVar Annotator: match by term: NEPHROLITHIASIS, HYPERCALCIURIC, X-LINKED | ClinVar Annotator: match by term: Nephrolithiasis 2
CTD Direct Evidence: marker/mechanism		 ClinVar
CTD
OMIM		 PMID:7874126 PMID:7915957 PMID:8559248 PMID:8950885 PMID:9062355 More... NCBI chr  X:49,922,596...50,099,230
Ensembl chr  X:49,922,596...50,099,235 		JBrowse link
G LOC126863258 BRD4-independent group 4 enhancer GRCh37_chrX:49854497-49855696 IAGP ClinVar Annotator: match by term: Nephrolithiasis 2 ClinVar PMID:7874126 PMID:8559248 PMID:9062355 PMID:9259268 PMID:9328929 More... NCBI chr  X:50,089,840...50,091,039 JBrowse link
G LOC130068287 ATAC-STARR-seq lymphoblastoid silent region 20849 IAGP ClinVar Annotator: match by term: Nephrolithiasis 2 ClinVar PMID:7874126 PMID:9328929 PMID:15052463 NCBI chr  X:49,922,858...49,922,907 JBrowse link
G MIR188 microRNA 188 IAGP ClinVar Annotator: match by term: Nephrolithiasis 2 ClinVar PMID:7874126 PMID:9328929 PMID:15052463 NCBI chr  X:50,003,503...50,003,588
Ensembl chr  X:50,003,503...50,003,588 		JBrowse link
G MIR362 microRNA 362 IAGP ClinVar Annotator: match by term: Nephrolithiasis 2 ClinVar PMID:7874126 PMID:9328929 PMID:15052463 NCBI chr  X:50,008,964...50,009,028
Ensembl chr  X:50,008,964...50,009,028 		JBrowse link
G MIR500A microRNA 500a IAGP ClinVar Annotator: match by term: Nephrolithiasis 2 ClinVar PMID:7874126 PMID:9328929 PMID:15052463 NCBI chr  X:50,008,431...50,008,514
Ensembl chr  X:50,008,431...50,008,514 		JBrowse link
G MIR500B microRNA 500b IAGP ClinVar Annotator: match by term: Nephrolithiasis 2 ClinVar PMID:7874126 PMID:9328929 PMID:15052463 NCBI chr  X:50,010,672...50,010,750
Ensembl chr  X:50,010,672...50,010,750 		JBrowse link
G MIR501 microRNA 501 IAGP ClinVar Annotator: match by term: Nephrolithiasis 2 ClinVar PMID:7874126 PMID:9328929 PMID:15052463 NCBI chr  X:50,009,722...50,009,805
Ensembl chr  X:50,009,722...50,009,805 		JBrowse link
G MIR502 microRNA 502 IAGP ClinVar Annotator: match by term: Nephrolithiasis 2 ClinVar PMID:7874126 PMID:9328929 PMID:15052463 NCBI chr  X:50,014,598...50,014,683
Ensembl chr  X:50,014,598...50,014,683 		JBrowse link
G MIR532 microRNA 532 IAGP ClinVar Annotator: match by term: Nephrolithiasis 2 ClinVar PMID:7874126 PMID:9328929 PMID:15052463 NCBI chr  X:50,003,148...50,003,238
Ensembl chr  X:50,003,148...50,003,238 		JBrowse link
G MIR660 microRNA 660 IAGP ClinVar Annotator: match by term: Nephrolithiasis 2 ClinVar PMID:7874126 PMID:9328929 PMID:15052463 NCBI chr  X:50,013,241...50,013,337
Ensembl chr  X:50,013,241...50,013,337 		JBrowse link
Dent disease 2 term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G INPP5B inositol polyphosphate-5-phosphatase B IAGP ClinVar Annotator: match by term: Dent disease type 2 ClinVar PMID:28018608 NCBI chr 1:37,860,697...37,947,057
Ensembl chr 1:37,860,697...37,947,053 		JBrowse link
G LOC113875008 Sharpr-MPRA regulatory region 13828 IAGP ClinVar Annotator: match by term: Dent disease type 2 ClinVar PMID:25741868 PMID:28492532 NCBI chr  X:129,540,092...129,540,472 JBrowse link
G OCRL OCRL inositol polyphosphate-5-phosphatase IAGP
EXP		 ClinVar Annotator: match by term: Dent disease type 2
CTD Direct Evidence: marker/mechanism		 OMIM
ClinVar
CTD		 PMID:1321346 PMID:8504307 PMID:15627218 PMID:16381338 PMID:17162149 More... NCBI chr  X:129,540,259...129,592,556
Ensembl chr  X:129,539,849...129,592,561 		JBrowse link
Glycinuria with or without Oxalate Urolithiasis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G SLC36A1 solute carrier family 36 member 1 IAGP ClinVar Annotator: match by term: Hyperglycinuria ClinVar PMID:19033659 NCBI chr 5:151,344,596...151,556,085
Ensembl chr 5:151,437,046...151,492,379 		JBrowse link
G SLC36A2 solute carrier family 36 member 2 IAGP ClinVar Annotator: match by term: Hyperglycinuria
ClinVar Annotator: match by term: Hyperglycinuria | ClinVar Annotator: match by term: IMINOGLYCINURIA TYPE II		 ClinVar
OMIM		 PMID:19033659 PMID:25741868 PMID:28492532 NCBI chr 5:151,314,972...151,347,559
Ensembl chr 5:151,314,972...151,347,590 		JBrowse link
G SLC6A19 solute carrier family 6 member 19 IAGP ClinVar Annotator: match by term: IMINOGLYCINURIA TYPE II
ClinVar Annotator: match by term: Hyperglycinuria | ClinVar Annotator: match by term: IMINOGLYCINURIA TYPE II		 ClinVar PMID:9536098 PMID:15286787 PMID:15286788 PMID:16199547 PMID:17555458 More... NCBI chr 5:1,201,595...1,225,111
Ensembl chr 5:1,201,595...1,225,111 		JBrowse link
G SLC6A20 solute carrier family 6 member 20 IAGP ClinVar Annotator: match by term: Hyperglycinuria
ClinVar Annotator: match by term: Hyperglycinuria | ClinVar Annotator: match by term: IMINOGLYCINURIA TYPE II		 ClinVar PMID:19033659 PMID:25741868 PMID:28492532 NCBI chr 3:45,755,449...45,796,536
Ensembl chr 3:45,755,449...45,796,574 		JBrowse link
hypophosphatemic nephrolithiasis/osteoporosis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G F12 coagulation factor XII IAGP ClinVar Annotator: match by term: Nephrolithiasis/osteoporosis, hypophosphatemic ClinVar PMID:24033266 PMID:25050900 PMID:25741868 PMID:28492532 PMID:30943683 NCBI chr 5:177,402,141...177,409,564
Ensembl chr 5:177,402,133...177,416,583 		JBrowse link
G SLC34A1 solute carrier family 34 member 1 IAGP ClinVar Annotator: match by term: Nephrolithiasis/osteoporosis, hypophosphatemic ClinVar PMID:24033266 PMID:25050900 PMID:25741868 PMID:28492532 PMID:30943683 NCBI chr 5:177,384,434...177,398,848
Ensembl chr 5:177,379,235...177,398,848 		JBrowse link
hypophosphatemic nephrolithiasis/osteoporosis 1 term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G F12 coagulation factor XII IAGP ClinVar Annotator: match by term: Hypophosphatemic nephrolithiasis/osteoporosis 1 ClinVar PMID:25050900 PMID:25741868 PMID:28492532 PMID:30943683 NCBI chr 5:177,402,141...177,409,564
Ensembl chr 5:177,402,133...177,416,583 		JBrowse link
G SLC34A1 solute carrier family 34 member 1 IAGP ClinVar Annotator: match by term: Hypophosphatemic nephrolithiasis/osteoporosis 1 OMIM
ClinVar		 PMID:9536098 PMID:12324554 PMID:14672348 PMID:16199547 PMID:16688119 More... NCBI chr 5:177,384,434...177,398,848
Ensembl chr 5:177,379,235...177,398,848 		JBrowse link
G SLC34A3 solute carrier family 34 member 3 IAGP ClinVar Annotator: match by term: Hypophosphatemic nephrolithiasis/osteoporosis 1 ClinVar PMID:25741868 PMID:28492532 PMID:31672324 NCBI chr 9:137,229,730...137,236,555
Ensembl chr 9:137,230,757...137,236,555 		JBrowse link
hypophosphatemic nephrolithiasis/osteoporosis 2 term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G NHERF1 NHERF family PDZ scaffold protein 1 IAGP ClinVar Annotator: match by term: Hypophosphatemic nephrolithiasis/osteoporosis 2 OMIM
ClinVar		 PMID:18784102 PMID:24033266 PMID:25326635 PMID:25741868 PMID:28492532 More... NCBI chr17:74,748,628...74,769,353
Ensembl chr17:74,748,628...74,769,353 		JBrowse link
G SLC9A3R1-AS1 SLC9A3R1 antisense RNA 1 IAGP ClinVar Annotator: match by term: Hypophosphatemic nephrolithiasis/osteoporosis 2 ClinVar PMID:18784102 PMID:25741868 PMID:28492532 NCBI chr17:74,745,600...74,749,867 JBrowse link
hypotonia-cystinuria syndrome term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G CAMKMT calmodulin-lysine N-methyltransferase EXP
ISS		 CTD Direct Evidence: marker/mechanism
OMIM:606407		 CTD
MouseDO		 PMID:26247364 NCBI chr 2:44,361,947...44,772,592
Ensembl chr 2:44,361,947...44,772,592 		JBrowse link
G PPM1B protein phosphatase, Mg2+/Mn2+ dependent 1B EXP CTD Direct Evidence: marker/mechanism CTD PMID:26247364 NCBI chr 2:44,168,875...44,246,928
Ensembl chr 2:44,167,969...44,244,384 		JBrowse link
G PREPL prolyl endopeptidase like EXP CTD Direct Evidence: marker/mechanism CTD PMID:26247364 NCBI chr 2:44,317,607...44,361,862
Ensembl chr 2:44,316,281...44,361,862 		JBrowse link
G SLC3A1 solute carrier family 3 member 1 EXP CTD Direct Evidence: marker/mechanism CTD PMID:26247364 NCBI chr 2:44,275,480...44,322,437
Ensembl chr 2:44,275,458...44,321,494 		JBrowse link
Kidney Calculi term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G BGLAP bone gamma-carboxyglutamate protein ISO RGD PMID:12674322 RGD:7207412 NCBI chr 1:156,242,184...156,243,317
Ensembl chr 1:156,242,184...156,243,317 		JBrowse link
G CA2 carbonic anhydrase 2 ISO RGD PMID:10977795 RGD:1600710 NCBI chr 8:85,464,007...85,481,493
Ensembl chr 8:85,463,968...85,481,493 		JBrowse link
G CAT catalase EXP CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr11:34,438,934...34,472,060
Ensembl chr11:34,438,934...34,472,060 		JBrowse link
G CD44 CD44 molecule (IN blood group) ISO RGD PMID:16850024 RGD:2289370 NCBI chr11:35,139,171...35,232,402
Ensembl chr11:35,138,882...35,232,402 		JBrowse link
G CLDN14 claudin 14 EXP CTD Direct Evidence: marker/mechanism CTD PMID:19561606 NCBI chr21:36,460,621...36,576,569
Ensembl chr21:36,460,621...36,576,569 		JBrowse link
G F2 coagulation factor II, thrombin susceptibility IAGP DNA:haplotypes: : RGD PMID:21067798 RGD:6893526 NCBI chr11:46,719,213...46,739,506
Ensembl chr11:46,719,196...46,739,506 		JBrowse link
G GSTP1 glutathione S-transferase pi 1 EXP CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr11:67,583,812...67,586,653
Ensembl chr11:67,583,742...67,586,656 		JBrowse link
G IFNG interferon gamma ISO associated with type 2 diabetes mellitus; mRNA:increased expression:kidney RGD PMID:21514417 RGD:6893463 NCBI chr12:68,154,768...68,159,740
Ensembl chr12:68,154,768...68,159,740 		JBrowse link
G MGP matrix Gla protein ISO RGD PMID:10460895 RGD:1582511 NCBI chr12:14,880,864...14,885,854
Ensembl chr12:14,880,864...14,885,857 		JBrowse link
G MPO myeloperoxidase IEP protein:increased activity:blood RGD PMID:18022927 RGD:7174700 NCBI chr17:58,269,855...58,280,935
Ensembl chr17:58,269,855...58,280,935 		JBrowse link
G POMC proopiomelanocortin EXP CTD Direct Evidence: marker/mechanism CTD PMID:1324751 NCBI chr 2:25,160,860...25,168,580
Ensembl chr 2:25,160,853...25,168,903 		JBrowse link
G SOD1 superoxide dismutase 1 EXP CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr21:31,659,693...31,668,931
Ensembl chr21:31,659,666...31,668,931 		JBrowse link
G SPP1 secreted phosphoprotein 1 IDA
EXP
ISO		 CTD Direct Evidence: marker/mechanism CTD
RGD		 PMID:8325891 PMID:10890885 PMID:15954903 PMID:21378157 PMID:16105024 RGD:1581372, RGD:6903839, RGD:1581334 NCBI chr 4:87,975,714...87,983,411
Ensembl chr 4:87,975,667...87,983,532 		JBrowse link
G TRPM7 transient receptor potential cation channel subfamily M member 7 EXP CTD Direct Evidence: marker/mechanism CTD PMID:24291744 NCBI chr15:50,557,158...50,686,797
Ensembl chr15:50,552,473...50,686,797 		JBrowse link
low molecular weight proteinuria with hypercalciuric nephrocalcinosis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G CLCN5 chloride voltage-gated channel 5 IAGP
EXP		 ClinVar Annotator: match by term: Proteinuria, low molecular weight, with hypercalciuria and nephrocalcinosis
CTD Direct Evidence: marker/mechanism		 ClinVar
CTD
OMIM		 PMID:7915957 PMID:8559248 PMID:9062355 PMID:9187673 PMID:9734595 More... NCBI chr  X:49,922,596...50,099,230
Ensembl chr  X:49,922,596...50,099,235 		JBrowse link
G LOC126863258 BRD4-independent group 4 enhancer GRCh37_chrX:49854497-49855696 IAGP ClinVar Annotator: match by term: Proteinuria, low molecular weight, with hypercalciuria and nephrocalcinosis ClinVar PMID:9062355 PMID:11136179 PMID:15719255 PMID:15895257 PMID:16822791 More... NCBI chr  X:50,089,840...50,091,039 JBrowse link
nephrolithiasis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G AGXT alanine--glyoxylate aminotransferase IAGP ClinVar Annotator: match by term: Nephrolithiasis ClinVar PMID:9192270 PMID:10541294 PMID:10960483 PMID:12777626 PMID:15327387 More... NCBI chr 2:240,868,824...240,880,500
Ensembl chr 2:240,868,824...240,880,502 		JBrowse link
G AHSG alpha 2-HS glycoprotein IAGP ClinVar Annotator: match by term: Calcium oxalate urolithiasis ClinVar PMID:24886237 NCBI chr 3:186,613,060...186,621,318
Ensembl chr 3:186,613,060...186,621,318 		JBrowse link
G BGLAP bone gamma-carboxyglutamate protein IAGP ClinVar Annotator: match by term: Calcium oxalate urolithiasis ClinVar PMID:24886237 NCBI chr 1:156,242,184...156,243,317
Ensembl chr 1:156,242,184...156,243,317 		JBrowse link
G CASR calcium sensing receptor IAGP DNA:snps, haplotypes:multiple (human) RGD PMID:20067903 RGD:7205448 NCBI chr 3:122,183,668...122,291,629
Ensembl chr 3:122,183,668...122,291,629 		JBrowse link
G CD44 CD44 molecule (IN blood group) IAGP ClinVar Annotator: match by term: Calcium oxalate urolithiasis ClinVar PMID:24886237 NCBI chr11:35,139,171...35,232,402
Ensembl chr11:35,138,882...35,232,402 		JBrowse link
G CYP24A1 cytochrome P450 family 24 subfamily A member 1 EXP CTD Direct Evidence: marker/mechanism CTD PMID:22337913 NCBI chr20:54,143,538...54,173,986
Ensembl chr20:54,153,446...54,173,986 		JBrowse link
G GSR glutathione-disulfide reductase ISO RGD PMID:16670437 RGD:7257558 NCBI chr 8:30,678,066...30,727,846
Ensembl chr 8:30,678,066...30,727,846 		JBrowse link
G HAO1 hydroxyacid oxidase 1 IAGP ClinVar Annotator: match by term: Calcium oxalate urolithiasis ClinVar PMID:24886237 NCBI chr20:7,882,985...7,940,458
Ensembl chr20:7,882,985...7,940,458 		JBrowse link
G IDUA alpha-L-iduronidase IAGP ClinVar Annotator: match by term: Calcium oxalate urolithiasis
ClinVar Annotator: match by term: Calcium oxalate nephrolithiasis | ClinVar Annotator: match by term: Calcium oxalate urolithiasis		 ClinVar PMID:25741868 PMID:27125215 PMID:27210743 PMID:27238910 PMID:27939258 More... NCBI chr 4:986,997...1,008,351
Ensembl chr 4:986,997...1,004,564 		JBrowse link
G MT-CO3 mitochondrially encoded cytochrome c oxidase III IAGP ClinVar Annotator: match by term: Nephrolithiasis ClinVar PMID:25741868 NCBI chr MT:9,207...9,990
Ensembl chr MT:9,207...9,990 		JBrowse link
G NHERF1 NHERF family PDZ scaffold protein 1 IAGP ClinVar Annotator: match by term: Nephrolithiasis ClinVar PMID:18784102 PMID:24033266 PMID:28492532 PMID:28893421 NCBI chr17:74,748,628...74,769,353
Ensembl chr17:74,748,628...74,769,353 		JBrowse link
G PAQR6 progestin and adipoQ receptor family member 6 IAGP ClinVar Annotator: match by term: Calcium oxalate urolithiasis ClinVar PMID:24886237 NCBI chr 1:156,243,320...156,248,056
Ensembl chr 1:156,243,320...156,248,117 		JBrowse link
G RGS14 regulator of G protein signaling 14 IAGP DNA:SNP: :rs11746443 (human) RGD PMID:22396660 RGD:7242927 NCBI chr 5:177,357,924...177,372,596
Ensembl chr 5:177,357,924...177,372,596 		JBrowse link
G SLC25A25 solute carrier family 25 member 25 IAGP ClinVar Annotator: match by term: Nephrolithiasis ClinVar NCBI chr 9:128,068,232...128,109,245
Ensembl chr 9:128,068,201...128,109,245 		JBrowse link
G SLC26A1 solute carrier family 26 member 1 IAGP ClinVar Annotator: match by term: Calcium oxalate urolithiasis
ClinVar Annotator: match by term: Calcium oxalate nephrolithiasis
ClinVar Annotator: match by term: Calcium oxalate nephrolithiasis | ClinVar Annotator: match by term: Calcium oxalate urolithiasis		 ClinVar PMID:25741868 PMID:27125215 PMID:27210743 PMID:27238910 PMID:27939258 More... NCBI chr 4:978,991...993,404
Ensembl chr 4:979,073...993,440 		JBrowse link
G SLC34A1 solute carrier family 34 member 1 onset IAGP
ISO		 DNA:snp:intron:IVS4+54C>T rs3812036 (human)
ClinVar Annotator: match by term: Nephrolithiasis
associated with Hyperoxaluria		 ClinVar
RGD		 PMID:16199547 PMID:25741868 PMID:26047794 PMID:28492532 PMID:28893421 More... RGD:7242927, RGD:7243005 NCBI chr 5:177,384,434...177,398,848
Ensembl chr 5:177,379,235...177,398,848 		JBrowse link
G SNORD164 small nucleolar RNA, C/D box 164 IAGP ClinVar Annotator: match by term: Calcium oxalate urolithiasis ClinVar PMID:24886237 NCBI chr11:35,162,950...35,163,010 JBrowse link
G TGFB1 transforming growth factor beta 1 treatment ISO RGD PMID:24712822 RGD:11073675 NCBI chr19:41,330,323...41,353,922
Ensembl chr19:41,301,587...41,353,922 		JBrowse link
prostate calculus term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G LTF lactotransferrin IEP RGD PMID:19202053 RGD:7243107 NCBI chr 3:46,435,645...46,485,234
Ensembl chr 3:46,435,645...46,485,234 		JBrowse link
Renal Hypouricemia term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G SLC22A12 solute carrier family 22 member 12 IAGP
EXP		 ClinVar Annotator: match by term: Dalmatian hypouricemia | ClinVar Annotator: match by term: Renal hypouricemia
CTD Direct Evidence: marker/mechanism		 OMIM
ClinVar
CTD		 PMID:12024214 PMID:14655203 PMID:14694169 PMID:15054642 PMID:15327384 More... NCBI chr11:64,591,220...64,602,344
Ensembl chr11:64,590,641...64,602,353 		JBrowse link
G SLC2A9 solute carrier family 2 member 9 EXP
IAGP		 CTD Direct Evidence: marker/mechanism
ClinVar Annotator: match by term: Dalmatian hypouricemia		 CTD
ClinVar		 PMID:18989453 PMID:22132990 NCBI chr 4:9,771,025...10,040,270
Ensembl chr 4:9,771,153...10,054,936 		JBrowse link
Ureteral Calculi term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G CAT catalase EXP CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr11:34,438,934...34,472,060
Ensembl chr11:34,438,934...34,472,060 		JBrowse link
G GSR glutathione-disulfide reductase EXP CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr 8:30,678,066...30,727,846
Ensembl chr 8:30,678,066...30,727,846 		JBrowse link
G GSTP1 glutathione S-transferase pi 1 EXP CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr11:67,583,812...67,586,653
Ensembl chr11:67,583,742...67,586,656 		JBrowse link
G SOD1 superoxide dismutase 1 EXP CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr21:31,659,693...31,668,931
Ensembl chr21:31,659,666...31,668,931 		JBrowse link
uric acid nephrolithiasis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G LOC126860945 BRD4-independent group 4 enhancer GRCh37_chr10:64414839-64416038 IAGP ClinVar Annotator: match by term: Nephrolithiasis, uric acid, susceptibility to ClinVar PMID:12740763 PMID:28492532 NCBI chr10:62,655,079...62,656,278 JBrowse link
G ZNF365 zinc finger protein 365 susceptibility IAGP ClinVar Annotator: match by term: Nephrolithiasis, uric acid, susceptibility to OMIM
ClinVar		 PMID:12740763 PMID:28492532 NCBI chr10:62,374,369...62,480,285
Ensembl chr10:62,374,192...62,480,288 		JBrowse link
Urinary Calculi term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G ADD3 adducin 3 ISO RGD PMID:15329129 RGD:2317717 NCBI chr10:109,996,373...110,135,565
Ensembl chr10:109,996,368...110,135,565 		JBrowse link
G F2 coagulation factor II, thrombin IDA RGD PMID:22494008 RGD:6893519 NCBI chr11:46,719,213...46,739,506
Ensembl chr11:46,719,196...46,739,506 		JBrowse link
G IL1RN interleukin 1 receptor antagonist susceptibility IAGP DNA:repeats, haplotype:intron:IVS2+914_1000dup IL1RN*1, IL1RN*2 IL1RN*3 (human) RGD PMID:18186699 RGD:6907399 NCBI chr 2:113,099,360...113,134,014
Ensembl chr 2:113,099,315...113,134,016 		JBrowse link
G SPP1 secreted phosphoprotein 1 no_association IAGP DNA:polymorphism: :p.R9402H (human)
DNA:polymorphism: :p.N9171S (human)		 RGD PMID:16145474 PMID:16145474 RGD:1581368, RGD:1581368 NCBI chr 4:87,975,714...87,983,411
Ensembl chr 4:87,975,667...87,983,532 		JBrowse link
G VDR vitamin D receptor IEA GAD PMID:15118671 RGD:1331525 NCBI chr12:47,841,537...47,904,994
Ensembl chr12:47,841,537...47,943,048 		JBrowse link
X-linked nephrolithiasis type I term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G CLCN5 chloride voltage-gated channel 5 IAGP
EXP		 ClinVar Annotator: match by term: X-linked recessive nephrolithiasis with renal failure
ClinVar Annotator: match by term: UROLITHIASIS, X-LINKED RECESSIVE, TYPE 1 | ClinVar Annotator: match by term: X-linked recessive nephrolithiasis with renal failure
CTD Direct Evidence: marker/mechanism		 ClinVar
CTD
OMIM		 PMID:7915957 PMID:8559248 PMID:9187673 PMID:9602200 PMID:9734595 More... NCBI chr  X:49,922,596...50,099,230
Ensembl chr  X:49,922,596...50,099,235 		JBrowse link
G LOC126863258 BRD4-independent group 4 enhancer GRCh37_chrX:49854497-49855696 IAGP ClinVar Annotator: match by term: UROLITHIASIS, X-LINKED RECESSIVE, TYPE 1
ClinVar Annotator: match by term: UROLITHIASIS, X-LINKED RECESSIVE, TYPE 1 | ClinVar Annotator: match by term: X-linked recessive nephrolithiasis with renal failure		 ClinVar PMID:8559248 PMID:11136179 PMID:15719255 PMID:15895257 PMID:16822791 More... NCBI chr  X:50,089,840...50,091,039 JBrowse link
Term paths to the root
Path 1
Term Annotations click to browse term
  disease 97387
    disease of anatomical entity 91016
      Urogenital Diseases 13189
        urinary system disease 4319
          urolithiasis 200
            Glycinuria with or without Oxalate Urolithiasis 4
            Urinary Calculi + 22
            adenine phosphoribosyltransferase deficiency 4
            cystinuria + 7
            nephrolithiasis + 177
            ureterolithiasis + 4
            uric acid urolithiasis 0
paths to the root